X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FYPPDB ENTRY 5FYP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP10PEG3350 24-27%, CAPS/BICINE MIX PH 9.0-10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, 24 WELL PLATE, HANGING DROPS
Crystal Properties
Matthews coefficientSolvent content
1.9938.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.443α = 90
b = 135.443β = 90
c = 113.732γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4548.9399.70.0714.57.21841752
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4795.20.62.55.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5FYP1.4548.93174938915999.680.147220.144880.19184RANDOM16.818
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.07-0.070.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.774
r_sphericity_free27.31
r_dihedral_angle_4_deg16.4
r_dihedral_angle_3_deg11.608
r_sphericity_bonded9.027
r_dihedral_angle_1_deg6.327
r_rigid_bond_restr4.143
r_long_range_B_refined3.962
r_long_range_B_other3.925
r_scangle_other3.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.774
r_sphericity_free27.31
r_dihedral_angle_4_deg16.4
r_dihedral_angle_3_deg11.608
r_sphericity_bonded9.027
r_dihedral_angle_1_deg6.327
r_rigid_bond_restr4.143
r_long_range_B_refined3.962
r_long_range_B_other3.925
r_scangle_other3.216
r_scbond_it2.708
r_scbond_other2.708
r_mcangle_other2.146
r_mcangle_it2.145
r_mcbond_it1.877
r_mcbond_other1.876
r_angle_refined_deg1.666
r_angle_other_deg1.101
r_chiral_restr0.468
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9065
Nucleic Acid Atoms
Solvent Atoms1072
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing